Load MOFA models

MOFA model SIMPLE

plotDataOverview(MOFA_simple)

Analyze trained MOFA model

# Calculate the variance explained (R2) per factor in each view 
r2 <- calculateVarianceExplained(MOFA_simple)
r2$R2Total
##    CyTOF_exp RNA_topgenes     mutation 
##   0.11896905   0.43082302   0.06067289
# Variance explained by each factor in each view
head(r2$R2PerFactor)
##        CyTOF_exp RNA_topgenes     mutation
## LF1 1.310245e-02   0.10388835 6.019647e-02
## LF2 8.866526e-02   0.04208622 5.061156e-05
## LF3 5.075316e-04   0.09063537 5.523796e-05
## LF4 1.033843e-04   0.05257305 4.547213e-05
## LF5 1.605860e-02   0.02319636 6.661611e-05
## LF6 8.632895e-05   0.03475225 7.062582e-05
# Plot it
plotVarianceExplained(MOFA_simple)

Characterization of individual factors

CyTOF expression

plotWeightsHeatmap(
  MOFA_simple, 
  view = "CyTOF_exp", 
  factors = 1:5,
  show_colnames = FALSE, main = 'CyTOF_exp'
)

plotTopWeights(
  MOFA_simple, 
  view="CyTOF_exp", 
  factor=2
)

plotTopWeights(
  MOFA_simple, 
  view="CyTOF_exp", 
  factor=1
)

plotTopWeights(
  MOFA_simple, 
  view="CyTOF_exp", 
  factor=5
)

RNA Seq Top genes

plotWeightsHeatmap(
  MOFA_simple, 
  view = "RNA_topgenes", 
  factors = 1:5,
  show_colnames = FALSE, main = 'RNA_topgenes'
)

plotTopWeights(
  MOFA_simple, 
  view="RNA_topgenes", 
  factor=1
)

plotTopWeights(
  MOFA_simple, 
  view="RNA_topgenes", 
  factor=2
)

plotTopWeights(
  MOFA_simple, 
  view="RNA_topgenes", 
  factor=3
)

WES

plotWeightsHeatmap(
  MOFA_simple, 
  view = "mutation", 
  factors = 1:5,
  show_colnames = F, main = 'Mutation Data'
)

plotTopWeights(
  MOFA_simple, 
  view="mutation", 
  factor=1
)

Feature set enrichment analysis in the active views

# Load reactome annotations
data("reactomeGS") # binary matrix with feature sets in rows and features in columns

# perform enrichment analysis
gsea <- runEnrichmentAnalysis(
  MOFA_simple,
  view = "RNA_topgenes",
  feature.sets = reactomeGS,
  alpha = 0.01
)
## Doing Feature Set Enrichment Analysis with the following options...
## View: RNA_topgenes
## Factors: LF1 LF2 LF3 LF4 LF5 LF6 LF7 LF8 LF9
## Number of feature sets: 640
## Local statistic: loading
## Transformation: abs.value
## Global statistic: mean.diff
## Statistical test: parametric
plotEnrichmentBars(gsea, alpha=0.01)

interestingFactors <- 1:2

fseaplots <- lapply(interestingFactors, function(factor) {
  plotEnrichment(
    MOFA_simple,
    gsea,
    factor = factor,
    alpha = 0.01,
    max.pathways = 10 # The top number of pathways to display
  )
})

cowplot::plot_grid(fseaplots[[1]], fseaplots[[2]],
                   ncol = 1, labels = paste("Factor", interestingFactors))

interestingFactors <- 3:4

fseaplots <- lapply(interestingFactors, function(factor) {
  plotEnrichment(
    MOFA_simple,
    gsea,
    factor = factor,
    alpha = 0.01,
    max.pathways = 10 # The top number of pathways to display
  )
})

cowplot::plot_grid(fseaplots[[1]], fseaplots[[2]],
                   ncol = 1, labels = paste("Factor", interestingFactors))

interestingFactors <- 5:6

fseaplots <- lapply(interestingFactors, function(factor) {
  plotEnrichment(
    MOFA_simple,
    gsea,
    factor = factor,
    alpha = 0.01,
    max.pathways = 10 # The top number of pathways to display
  )
})

cowplot::plot_grid(fseaplots[[1]], fseaplots[[2]],
                   ncol = 1, labels = paste("Factor", interestingFactors))

plotFactorScatters(
  MOFA_simple,
  factors = c(1:5),
  color_by = "TP53"
)
## Registered S3 method overwritten by 'GGally':
##   method from   
##   +.gg   ggplot2
## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

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## Warning: Removed 11 rows containing missing values (geom_point).

plotFactorScatters(
  MOFA_simple,
  factors = c(1:5),
  color_by = "KRAS"
)
## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

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## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

plotFactorScatters(
  MOFA_simple,
  factors = c(1:5),
  color_by = "EGFR"
)
## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

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## Warning: Removed 11 rows containing missing values (geom_point).

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## Warning: Removed 11 rows containing missing values (geom_point).

plotFactorScatters(
  MOFA_simple,
  factors = c(1:5),
  color_by = "Mye_174Yb_HLA.DR"
)
## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

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## Warning: Removed 11 rows containing missing values (geom_point).

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## Warning: Removed 11 rows containing missing values (geom_point).

plotFactorScatters(
  MOFA_simple,
  factors = c(1:5),
  color_by = "Tc_154Sm_CD45"
)
## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

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## Warning: Removed 11 rows containing missing values (geom_point).

plotFactorScatters(
  MOFA_simple,
  factors = c(1:5),
  color_by = "Tc_168Er_CD8"
)
## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

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plotFactorScatters(
  MOFA_simple,
  factors = c(1:5),
  color_by = "Epi_174Yb_HLA.DR"
)
## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

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plotFactorScatters(
  MOFA_simple,
  factors = c(1:5),
  color_by = "FMes_174Yb_HLA.DR"
)
## Warning: Removed 11 rows containing missing values (geom_point).

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## Warning: Removed 11 rows containing missing values (geom_point).

MOFA model SIMPLE 2

plotDataOverview(MOFA_simple2)

Analyze trained MOFA model

# Calculate the variance explained (R2) per factor in each view 
r2 <- calculateVarianceExplained(MOFA_simple2)
r2$R2Total
##  CyTOF_prcnt RNA_topgenes     mutation 
##   0.03829975   0.43071879   0.06079154
# Variance explained by each factor in each view
head(r2$R2PerFactor)
##      CyTOF_prcnt RNA_topgenes     mutation
## LF1 0.0139093571   0.10400881 6.027968e-02
## LF2 0.0009794348   0.09060074 5.498855e-05
## LF3 0.0052959796   0.05252956 4.739019e-05
## LF4 0.0006543602   0.04194804 8.133970e-05
## LF5 0.0022720214   0.03479404 7.135350e-05
## LF6 0.0137766187   0.02318487 6.811659e-05
# Plot it
plotVarianceExplained(MOFA_simple2)

Characterization of individual factors

CyTOF percentage

plotWeightsHeatmap(
  MOFA_simple2, 
  view = "CyTOF_prcnt", 
  factors = 1:6,
  show_colnames = FALSE, main = 'CyTOF_prcnt'
)

plotTopWeights(
  MOFA_simple2, 
  view="CyTOF_prcnt", 
  factor=1
)

plotTopWeights(
  MOFA_simple2, 
  view="CyTOF_prcnt", 
  factor=3
)

plotTopWeights(
  MOFA_simple2, 
  view="CyTOF_prcnt", 
  factor=6
)

RNA Seq Top genes

plotWeightsHeatmap(
  MOFA_simple2, 
  view = "RNA_topgenes", 
  factors = 1:6,
  show_colnames = FALSE, main = 'RNA_topgenes'
)

plotTopWeights(
  MOFA_simple2, 
  view="RNA_topgenes", 
  factor=1
)

plotTopWeights(
  MOFA_simple2, 
  view="RNA_topgenes", 
  factor=2
)

plotTopWeights(
  MOFA_simple2, 
  view="RNA_topgenes", 
  factor=3
)

WES

plotWeightsHeatmap(
  MOFA_simple2, 
  view = "mutation", 
  factors = 1:6,
  show_colnames = F, main = 'Mutation Data'
)

plotTopWeights(
  MOFA_simple2, 
  view="mutation", 
  factor=1
)

Feature set enrichment analysis in the active views

# Load reactome annotations
data("reactomeGS") # binary matrix with feature sets in rows and features in columns

# perform enrichment analysis
gsea <- runEnrichmentAnalysis(
  MOFA_simple2,
  view = "RNA_topgenes",
  feature.sets = reactomeGS,
  alpha = 0.01
)
## Doing Feature Set Enrichment Analysis with the following options...
## View: RNA_topgenes
## Factors: LF1 LF2 LF3 LF4 LF5 LF6 LF7 LF8 LF9
## Number of feature sets: 640
## Local statistic: loading
## Transformation: abs.value
## Global statistic: mean.diff
## Statistical test: parametric
plotEnrichmentBars(gsea, alpha=0.01)

interestingFactors <- 1:2

fseaplots <- lapply(interestingFactors, function(factor) {
  plotEnrichment(
    MOFA_simple2,
    gsea,
    factor = factor,
    alpha = 0.01,
    max.pathways = 10 # The top number of pathways to display
  )
})

cowplot::plot_grid(fseaplots[[1]], fseaplots[[2]],
                   ncol = 1, labels = paste("Factor", interestingFactors))

interestingFactors <- 3:4

fseaplots <- lapply(interestingFactors, function(factor) {
  plotEnrichment(
    MOFA_simple2,
    gsea,
    factor = factor,
    alpha = 0.01,
    max.pathways = 10 # The top number of pathways to display
  )
})

cowplot::plot_grid(fseaplots[[1]], fseaplots[[2]],
                   ncol = 1, labels = paste("Factor", interestingFactors))

interestingFactors <- 5:6

fseaplots <- lapply(interestingFactors, function(factor) {
  plotEnrichment(
    MOFA_simple2,
    gsea,
    factor = factor,
    alpha = 0.01,
    max.pathways = 10 # The top number of pathways to display
  )
})

cowplot::plot_grid(fseaplots[[1]], fseaplots[[2]],
                   ncol = 1, labels = paste("Factor", interestingFactors))

plotFactorScatters(
  MOFA_simple2,
  factors = c(1:5),
  color_by = "TP53"
)
## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

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## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

plotFactorScatters(
  MOFA_simple2,
  factors = c(1:5),
  color_by = "KRAS"
)
## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

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## Warning: Removed 11 rows containing missing values (geom_point).

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## Warning: Removed 11 rows containing missing values (geom_point).

plotFactorScatters(
  MOFA_simple2,
  factors = c(1:5),
  color_by = "EGFR"
)
## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

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## Warning: Removed 11 rows containing missing values (geom_point).

plotFactorScatters(
  MOFA_simple2,
  factors = c(1:5),
  color_by = "Epithelial_10"
)
## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

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## Warning: Removed 11 rows containing missing values (geom_point).

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## Warning: Removed 11 rows containing missing values (geom_point).

plotFactorScatters(
  MOFA_simple2,
  factors = c(1:5),
  color_by = "Epithelial_1"
)
## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

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## Warning: Removed 11 rows containing missing values (geom_point).

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## Warning: Removed 11 rows containing missing values (geom_point).

plotFactorScatters(
  MOFA_simple2,
  factors = c(1:5),
  color_by = "Endothelial"
)
## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

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## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

plotFactorScatters(
  MOFA_simple2,
  factors = c(1:5),
  color_by = "Endothelial"
)
## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

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## Warning: Removed 11 rows containing missing values (geom_point).

plotFactorScatter(
  MOFA_simple2,
  factors = 1:2, dot_size = 3,
  color_by = "TP53",      # color by the IGHV values that are part of the training data
)

plotFactorScatter(
  MOFA_simple2,
  factors = 1:2, dot_size = 3,
  color_by = "ENSG00000060718",
  name_color = 'COL11A1'
)

plotFactorScatter(
  MOFA_simple2,
  factors = 1:2, dot_size = 3,
  color_by = "Epithelial_1",     
)

MOFA model SIMPLE 3

plotDataOverview(MOFA_simple3)

Analyze trained MOFA model

# Calculate the variance explained (R2) per factor in each view 
r2 <- calculateVarianceExplained(MOFA_simple3)
r2$R2Total
##    CyTOF_exp  CyTOF_prcnt RNA_topgenes     mutation 
##   0.12115006   0.06906895   0.43082705   0.06064075
# Variance explained by each factor in each view
head(r2$R2PerFactor)
##        CyTOF_exp  CyTOF_prcnt RNA_topgenes     mutation
## LF1 1.259907e-02 0.0144383661   0.10388770 6.016669e-02
## LF2 8.989940e-02 0.0274677976   0.04209575 4.993764e-05
## LF3 4.733282e-04 0.0009442448   0.09060997 5.514935e-05
## LF4 1.740497e-02 0.0179105781   0.02318013 6.548418e-05
## LF5 1.311077e-04 0.0054420308   0.05259932 4.527307e-05
## LF6 8.860807e-05 0.0017749235   0.03474953 7.050227e-05
# Plot it
plotVarianceExplained(MOFA_simple3)

Characterization of individual factors

CyTOF expression

plotWeightsHeatmap(
  MOFA_simple3, 
  view = "CyTOF_exp", 
  factors = 1:5,
  show_colnames = FALSE, main = 'CyTOF_exp'
)

plotTopWeights(
  MOFA_simple3, 
  view="CyTOF_exp", 
  factor=2
)

plotTopWeights(
  MOFA_simple3, 
  view="CyTOF_exp", 
  factor=1
)

plotTopWeights(
  MOFA_simple3, 
  view="CyTOF_exp", 
  factor=5
)

CyTOF percentage

plotWeightsHeatmap(
  MOFA_simple2, 
  view = "CyTOF_prcnt", 
  factors = 1:6,
  show_colnames = FALSE, main = 'CyTOF_prcnt'
)

plotTopWeights(
  MOFA_simple2, 
  view="CyTOF_prcnt", 
  factor=1
)

plotTopWeights(
  MOFA_simple2, 
  view="CyTOF_prcnt", 
  factor=3
)

plotTopWeights(
  MOFA_simple2, 
  view="CyTOF_prcnt", 
  factor=6
)

RNA Seq Top genes

plotWeightsHeatmap(
  MOFA_simple3, 
  view = "RNA_topgenes", 
  factors = 1:5,
  show_colnames = FALSE, main = 'RNA_topgenes'
)

plotTopWeights(
  MOFA_simple3, 
  view="RNA_topgenes", 
  factor=1
)

plotTopWeights(
  MOFA_simple3, 
  view="RNA_topgenes", 
  factor=2
)

plotTopWeights(
  MOFA_simple3, 
  view="RNA_topgenes", 
  factor=3
)

WES

plotWeightsHeatmap(
  MOFA_simple3, 
  view = "mutation", 
  factors = 1:5,
  show_colnames = F, main = 'Mutation Data'
)

plotTopWeights(
  MOFA_simple3, 
  view="mutation", 
  factor=1
)

Feature set enrichment analysis in the active views

# Load reactome annotations
data("reactomeGS") # binary matrix with feature sets in rows and features in columns

# perform enrichment analysis
gsea <- runEnrichmentAnalysis(
  MOFA_simple3,
  view = "RNA_topgenes",
  feature.sets = reactomeGS,
  alpha = 0.01
)
## Doing Feature Set Enrichment Analysis with the following options...
## View: RNA_topgenes
## Factors: LF1 LF2 LF3 LF4 LF5 LF6 LF7 LF8 LF9
## Number of feature sets: 640
## Local statistic: loading
## Transformation: abs.value
## Global statistic: mean.diff
## Statistical test: parametric
plotEnrichmentBars(gsea, alpha=0.01)

interestingFactors <- 1:2

fseaplots <- lapply(interestingFactors, function(factor) {
  plotEnrichment(
    MOFA_simple3,
    gsea,
    factor = factor,
    alpha = 0.01,
    max.pathways = 10 # The top number of pathways to display
  )
})

cowplot::plot_grid(fseaplots[[1]], fseaplots[[2]],
                   ncol = 1, labels = paste("Factor", interestingFactors))

interestingFactors <- 3:4

fseaplots <- lapply(interestingFactors, function(factor) {
  plotEnrichment(
    MOFA_simple3,
    gsea,
    factor = factor,
    alpha = 0.01,
    max.pathways = 10 # The top number of pathways to display
  )
})

cowplot::plot_grid(fseaplots[[1]], fseaplots[[2]],
                   ncol = 1, labels = paste("Factor", interestingFactors))

interestingFactors <- 5:6

fseaplots <- lapply(interestingFactors, function(factor) {
  plotEnrichment(
    MOFA_simple3,
    gsea,
    factor = factor,
    alpha = 0.01,
    max.pathways = 10 # The top number of pathways to display
  )
})

cowplot::plot_grid(fseaplots[[1]], fseaplots[[2]],
                   ncol = 1, labels = paste("Factor", interestingFactors))

plotFactorScatters(
  MOFA_simple3,
  factors = c(1:5),
  color_by = "TP53"
)
## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

plotFactorScatters(
  MOFA_simple3,
  factors = c(1:5),
  color_by = "KRAS"
)
## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

plotFactorScatters(
  MOFA_simple3,
  factors = c(1:5),
  color_by = "EGFR"
)
## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

plotFactorScatters(
  MOFA_simple3,
  factors = c(1:5),
  color_by = "Mye_174Yb_HLA.DR"
)
## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

plotFactorScatters(
  MOFA_simple3,
  factors = c(1:5),
  color_by = "Tc_154Sm_CD45"
)
## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

plotFactorScatters(
  MOFA_simple3,
  factors = c(1:5),
  color_by = "Tc_168Er_CD8"
)
## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

plotFactorScatters(
  MOFA_simple3,
  factors = c(1:5),
  color_by = "Epi_174Yb_HLA.DR"
)
## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

plotFactorScatters(
  MOFA_simple3,
  factors = c(1:5),
  color_by = "FMes_174Yb_HLA.DR"
)
## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

## Warning: Removed 11 rows containing missing values (geom_point).

MOFA model SIMPLE 4 (+ radiomics)

plotDataOverview(MOFA_simple4)

Analyze trained MOFA model

# Calculate the variance explained (R2) per factor in each view 
r2 <- calculateVarianceExplained(MOFA_simple4)
r2$R2Total
##  CyTOF_prcnt RNA_topgenes     mutation    radiomics 
##   0.03798793   0.43249415   0.05016605   0.23203561
# Variance explained by each factor in each view
head(r2$R2PerFactor)
##      CyTOF_prcnt RNA_topgenes     mutation    radiomics
## LF1 0.0101909453   0.10849324 4.969190e-02 3.172252e-02
## LF2 0.0123359808   0.05026874 2.369753e-05 4.889331e-02
## LF3 0.0080378676   0.09005975 8.527804e-05 3.628949e-05
## LF4 0.0023033604   0.03567126 3.388832e-05 4.631124e-02
## LF5 0.0002113700   0.04182733 3.142110e-05 3.510666e-02
## LF6 0.0006335965   0.03026588 2.776464e-05 4.512130e-02
# Plot it
plotVarianceExplained(MOFA_simple4)

Characterization of individual factors

CyTOF percentage

plotWeightsHeatmap(
  MOFA_simple4, 
  view = "CyTOF_prcnt", 
  factors = 1:6,
  show_colnames = FALSE, main = 'CyTOF_prcnt'
)

plotTopWeights(
  MOFA_simple4, 
  view="CyTOF_prcnt", 
  factor=1
)

plotTopWeights(
  MOFA_simple4, 
  view="CyTOF_prcnt", 
  factor=3
)

plotTopWeights(
  MOFA_simple4, 
  view="CyTOF_prcnt", 
  factor=6
)

RNA Seq Top genes

plotWeightsHeatmap(
  MOFA_simple4, 
  view = "RNA_topgenes", 
  factors = 1:6,
  show_colnames = FALSE, main = 'RNA_topgenes'
)

plotTopWeights(
  MOFA_simple4, 
  view="RNA_topgenes", 
  factor=1
)

plotTopWeights(
  MOFA_simple4, 
  view="RNA_topgenes", 
  factor=2
)

plotTopWeights(
  MOFA_simple4, 
  view="RNA_topgenes", 
  factor=3
)

WES

plotWeightsHeatmap(
  MOFA_simple4, 
  view = "mutation", 
  factors = 1:6,
  show_colnames = F, main = 'Mutation Data'
)

plotTopWeights(
  MOFA_simple4, 
  view="mutation", 
  factor=1
)

radiomics

plotWeightsHeatmap(
  MOFA_simple4, 
  view = "radiomics", 
  factors = 1:6,
  show_colnames = F, main = 'Radiomics Data'
)

plotTopWeights(
  MOFA_simple4, 
  view="radiomics", 
  factor=1
)

plotTopWeights(
  MOFA_simple4, 
  view="radiomics", 
  factor=2
)

Feature set enrichment analysis in the active views

# Load reactome annotations
data("reactomeGS") # binary matrix with feature sets in rows and features in columns

# perform enrichment analysis
gsea <- runEnrichmentAnalysis(
  MOFA_simple4,
  view = "RNA_topgenes",
  feature.sets = reactomeGS,
  alpha = 0.01
)
## Doing Feature Set Enrichment Analysis with the following options...
## View: RNA_topgenes
## Factors: LF1 LF2 LF3 LF4 LF5 LF6 LF7 LF8 LF9
## Number of feature sets: 640
## Local statistic: loading
## Transformation: abs.value
## Global statistic: mean.diff
## Statistical test: parametric
plotEnrichmentBars(gsea, alpha=0.01)

interestingFactors <- 1:2

fseaplots <- lapply(interestingFactors, function(factor) {
  plotEnrichment(
    MOFA_simple2,
    gsea,
    factor = factor,
    alpha = 0.01,
    max.pathways = 10 # The top number of pathways to display
  )
})

cowplot::plot_grid(fseaplots[[1]], fseaplots[[2]],
                   ncol = 1, labels = paste("Factor", interestingFactors))

interestingFactors <- 3:4

fseaplots <- lapply(interestingFactors, function(factor) {
  plotEnrichment(
    MOFA_simple4,
    gsea,
    factor = factor,
    alpha = 0.01,
    max.pathways = 10 # The top number of pathways to display
  )
})

cowplot::plot_grid(fseaplots[[1]], fseaplots[[2]],
                   ncol = 1, labels = paste("Factor", interestingFactors))

interestingFactors <- 5:6

fseaplots <- lapply(interestingFactors, function(factor) {
  plotEnrichment(
    MOFA_simple4,
    gsea,
    factor = factor,
    alpha = 0.01,
    max.pathways = 10 # The top number of pathways to display
  )
})

cowplot::plot_grid(fseaplots[[1]], fseaplots[[2]],
                   ncol = 1, labels = paste("Factor", interestingFactors))

plotFactorScatters(
  MOFA_simple4,
  factors = c(1:5),
  color_by = "TP53"
)
## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

plotFactorScatters(
  MOFA_simple4,
  factors = c(1:5),
  color_by = "KRAS"
)
## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

plotFactorScatters(
  MOFA_simple4,
  factors = c(1:5),
  color_by = "EGFR"
)
## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

plotFactorScatters(
  MOFA_simple4,
  factors = c(1:5),
  color_by = "Epithelial_10"
)
## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

plotFactorScatters(
  MOFA_simple4,
  factors = c(1:5),
  color_by = "Epithelial_1"
)
## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

plotFactorScatters(
  MOFA_simple4,
  factors = c(1:5),
  color_by = "Endothelial"
)
## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

plotFactorScatters(
  MOFA_simple4,
  factors = c(1:5),
  color_by = "Endothelial"
)
## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

## Warning: Removed 15 rows containing missing values (geom_point).

plotFactorScatter(
  MOFA_simple4,
  factors = 1:2, dot_size = 3,
  color_by = "TP53",      # color by the IGHV values that are part of the training data
)

plotFactorScatter(
  MOFA_simple4,
  factors = 1:2, dot_size = 3,
  color_by = "ENSG00000060718",
  name_color = 'COL11A1'
)

plotFactorScatter(
  MOFA_simple4,
  factors = 1:2, dot_size = 3,
  color_by = "Epithelial_1",     
)

plotFactorScatter(
  MOFA_simple4,
  factors = 1:2, dot_size = 3,
  color_by = "SILA_S",     
)